adding clinical review and updates to pnoc003

[kgaonkar6]

Purpose/implementation Section

What scientific question is your analysis addressing?

As part of molecular-subtype-HGG analysis we assign a HGG or DMG subtype from looking for K28M histone variants, in this PR we wanted to identifying samples which have differences between the clinically reviewed subtype and subtype from molecular-subtype-HGG module in PNOC003 and update those in the OpenPBTA subtyping module results

What was your approach?

The table from the original issue added by @jharenza is added as file in input folder. I used the file to check for changes and updated 3 WXS samples from PT_NK8A49X5, PT_QA9WJ679, PT_WGVEF96B by matching to the values in the reviewed files

What GitHub issue does your pull request address?

#751

Directions for reviewers. Tell potential reviewers what kind of feedback you are soliciting.

Which areas should receive a particularly close look?

I've created the file for v17 (which doesn't have subtypes for cell-lines) so I believe that will need to be updated once #797

Is there anything that you want to discuss further?

I've coded the checks specifically to only substitute and not assign H3 wildtype to DMG, H3 K28 if clinically the subtype was K28M mutant
https://github.com/kgaonkar6/OpenPBTA-analysis/blob/6e70a6795719007cd0233074b3fff7218d84bbb3/analyses/molecular-subtyping-HGG/10-pnoc003-clinical-review-update.Rmd#L145-L155

I did that because some subtypes have additional subtype like HGG IDH or BRAF V600 that need to be retained

Is the analysis in a mature enough form that the resulting figure(s) and/or table(s) are ready for review?

Yes

Results

What types of results are included (e.g., table, figure)?

table

What is your summary of the results?

results/HGG_molecular_subtype-clinical-review-update.tsv

Reproducibility Checklist

• The dependencies required to run the code in this pull request have been added to the project Dockerfile.
• This analysis has been added to continuous integration.

Documentation Checklist

• This analysis module has a README and it is up to date.
• This analysis is recorded in the table in analyses/README.md and the entry is up to date.
• The analytical code is documented and contains comments.

[jaclyn-taroni]

Thanks for filing this @kgaonkar6! I have not looked at this code in detail yet, but I would expect this addition to go into molecular-subtyping-pathology per the issue #751 and the discussion that preceded it (starts at #735 (comment)).

The rationale behind molecular-subtyping-pathology is to have a place to incorporate data or feedback outside of the "molecular rules" within OpenPBTA itself. Including the PNOC calls is within the scope of molecular-subtyping-pathology in my opinion.

Some thoughts where this functionality could go in that module rather than in molecular-subtyping-HGG:

• Be included as the first notebook in molecular-subtyping-pathology, prior to the compilation of all the subtyping results from all modules including HGG
• Get added to analyses/molecular-subtyping-pathology/02-incorporate-pathology-feedback.Rmd
• Get added as a separate notebook after analyses/molecular-subtyping-pathology/02-incorporate-pathology-feedback.Rmd

I'm not sure if I have a strong opinion or preference yet. Our goals for this should be to keep the notebooks at a size such that they are relatively easy to digest and the decision making process is clear, so I would say whatever place we think works best for those goals! I'm also going to need to address #784 and #667 within the next week or so, so we may change our minds about the exact position in that module as it evolves which is totally okay/to be expected.

[kgaonkar6]

Cool! I'll move it to molecular-subtyping-pathology as a separate notebook after analyses/molecular-subtyping-pathology/02-incorporate-pathology-feedback.Rmd.

Closing this PR